PXD056606

PXD056606 is an original dataset announced via ProteomeXchange.

Title	Potential of Proteomics in Forensic Phenotyping: A Focus on Biological Sex Determination
Description	Forensic DNA analysis is well established for phenotyping, providing valuable investigative leads. Recently, proteomics, the large-scale study of proteins, is increasingly recognized as a complementary tool to DNA analysis, particularly for enhancing the evidential value of traces and especially in cases involving degraded samples or challenging matrices. This study aims to extract phenotypic traits directly from whole blood proteomes, using biological sex determination as a starting point. Using LC–MS/MS, proteomes from 100 whole blood samples of known sex were used to train a biological sex classifier. Cross-validation of the model demonstrated the potential of proteomics for accurate sex classification. Key peptides, such as from pregnancy zone protein and ceruloplasmin, were identified as highly important features. To further evaluate the model, mock case samples were generated to simulate real-world case scenarios. However, a large portion of these mock samples were incorrectly classified, which was caused by batch effects. Based on our findings, transitioning from an untargeted assay to a maximally performant analytical targeted assay is the next crucial step needed for implementation into routine forensic application. Overall, this study advocates for the inclusion of proteomics as part of the forensic phenotyping toolkit, while addressing the challenges, opportunities, and recommendations in its implementation.
HostingRepository	PRIDE
AnnounceDate	2025-09-04
AnnouncementXML	Submission_2025-09-04_10:23:05.919.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Maarten Dhaenens
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	methylthiolated residue
Instrument	ZenoTOF 7600

Revision	Datetime	Status	ChangeLog Entry
0	2024-10-08 03:59:58	ID requested
⏵ 1	2025-09-04 10:23:06	announced

10.1021/ACS.JPROTEOME.5C00098;

submitter keyword: machine learning, proteomics, mass spectrometry,Forensic phenotyping, sex determination

Maarten Dhaenens
contact affiliation	ProGenTomics, Laboratory of Pharmaceutical Biotechnology, Ghent University, B-9000 Ghent, Belgium
contact email	maarten.dhaenens@ugent.be
lab head
Maarten Dhaenens
contact affiliation	Faculity of Pharmaceutical Biotechnology
contact email	maarten.dhaenens@ugent.be
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/09/PXD056606

PRIDE project URI

• PRIDE
  1. PXD056606
     1. Label: PRIDE project
     2. Name: Potential of Proteomics in Forensic Phenotyping: A Focus on Biological Sex Determination